+

X

Quality Statement

Pacific Biosciences is committed to providing high-quality products that meet customer expectations and comply with regulations. We will achieve these goals by adhering to and maintaining an effective quality-management system designed to ensure product quality, performance, and safety.

X

Image Use Agreement

By downloading, copying, or making any use of the images located on this website (“Site”) you acknowledge that you have read and understand, and agree to, the terms of this Image Usage Agreement, as well as the terms provided on the Legal Notices webpage, which together govern your use of the images as provided below. If you do not agree to such terms, do not download, copy or use the images in any way, unless you have written permission signed by an authorized Pacific Biosciences representative.

Subject to the terms of this Agreement and the terms provided on the Legal Notices webpage (to the extent they do not conflict with the terms of this Agreement), you may use the images on the Site solely for (a) editorial use by press and/or industry analysts, (b) in connection with a normal, peer-reviewed, scientific publication, book or presentation, or the like. You may not alter or modify any image, in whole or in part, for any reason. You may not use any image in a manner that misrepresents the associated Pacific Biosciences product, service or technology or any associated characteristics, data, or properties thereof. You also may not use any image in a manner that denotes some representation or warranty (express, implied or statutory) from Pacific Biosciences of the product, service or technology. The rights granted by this Agreement are personal to you and are not transferable by you to another party.

You, and not Pacific Biosciences, are responsible for your use of the images. You acknowledge and agree that any misuse of the images or breach of this Agreement will cause Pacific Biosciences irreparable harm. Pacific Biosciences is either an owner or licensee of the image, and not an agent for the owner. You agree to give Pacific Biosciences a credit line as follows: "Courtesy of Pacific Biosciences of California, Inc., Menlo Park, CA, USA" and also include any other credits or acknowledgments noted by Pacific Biosciences. You must include any copyright notice originally included with the images on all copies.

IMAGES ARE PROVIDED BY Pacific Biosciences ON AN "AS-IS" BASIS. Pacific Biosciences DISCLAIMS ALL REPRESENTATIONS AND WARRANTIES, EXPRESS, IMPLIED OR STATUTORY, INCLUDING, BUT NOT LIMITED TO, NON-INFRINGEMENT, OWNERSHIP, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. IN NO EVENT SHALL Pacific Biosciences BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, PUNITIVE, OR CONSEQUENTIAL DAMAGES OF ANY KIND WHATSOEVER WITH RESPECT TO THE IMAGES.

You agree that Pacific Biosciences may terminate your access to and use of the images located on the PacificBiosciences.com website at any time and without prior notice, if it considers you to have violated any of the terms of this Image Use Agreement. You agree to indemnify, defend and hold harmless Pacific Biosciences, its officers, directors, employees, agents, licensors, suppliers and any third party information providers to the Site from and against all losses, expenses, damages and costs, including reasonable attorneys' fees, resulting from any violation by you of the terms of this Image Use Agreement or Pacific Biosciences' termination of your access to or use of the Site. Termination will not affect Pacific Biosciences' rights or your obligations which accrued before the termination.

I have read and understand, and agree to, the Image Usage Agreement.

I disagree and would like to return to the Pacific Biosciences home page.

Pacific Biosciences
Contact:

Medicinal Plants: Investigating Biosynthesis with SMRT Sequencing

Tuesday, November 7, 2017

Photo of Panax ginseng by Eugene Kim

Three recent publications report results from transcriptome studies of plants often used for medicinal purposes, all powered by SMRT Sequencing and the Iso-Seq method. The papers on ginseng, Huangqi, and tea collectively show the importance of sequencing full-length isoforms for the most accurate and comprehensive gene expression analysis; they also demonstrate the usefulness of characterizing gene models for complex species in the absence of a reference genome assembly.

In “Isoform Sequencing Provides a More Comprehensive View of the Panax ginseng Transcriptome,” scientists from the National Institute of Horticultural and Herbal Science, Chungbuk National University, and other institutions in Korea describe efforts to characterize the functional genomics of P. ginseng. They studied four tissues (flower, leaf, stem, and root) from the ginseng plant, producing more than 135,000 assembled transcripts, averaging 3.2 kb in length. “We successfully identified unique full-length genes involved in triterpenoid saponin synthesis and plant hormonal signaling pathways, including auxin and cytokinin,” the team reports. “Transposable elements (TEs) were also identified, suggesting transcriptional activity of TEs in P. ginseng.” They also took a deep dive into 88 genes to assess alternative splicing. The scientists believe this work will facilitate the discovery of novel genes in this plant and its relatives, and suggest their results will be important for crop breeding programs.

Separately, scientists at the University of Adelaide in Australia and Shanxi University of Traditional Chinese Medicine in China published “Long read reference genome-free reconstruction of a full-length transcriptome from Astragalus membranaceus reveals transcript variants involved in bioactive compound biosynthesis.” A. membranaceus is also known as Huangqi and is a commonly used herb in Chinese medicine for cancers, diabetes, nephritis, and other diseases. The team studied transcriptomes of the plant’s leaf and root, identifying nearly 28,000 full-length, unique transcripts in leaf tissues and more than 22,000 in root tissues. “Compared with previous studies that used short read sequencing, our reconstructed transcripts are longer, and are more likely to be full-length and include numerous transcript variants,” the scientists report. Their analysis highlighted complex patterns of alternative splicing and enabled the detection of long-noncoding RNAs as well as characterization of biosynthesis genes. “Our study provides a practical pipeline to characterise the full-length transcriptome for species without a reference genome and a useful genomic resource for exploring the biosynthesis of active compounds in Astragalus membranaceus,” they conclude.

Finally, “Transcriptome Profiling Using Single-Molecule Direct RNA Sequencing Approach for In-depth Understanding of Genes in Secondary Metabolism Pathways of Camellia sinensis” comes from scientists at Anhui Agricultural University in China. They were investigating the biosynthesis of metabolites such as flavonoids and caffeine in this tea plant, performing Iso-Seq analysis of eight different tissues. The approach led to the identification of 94 full-length transcripts, plus four alternative splicing events, associated with the biosynthesis of the compounds of interest. “The longer reads improved the quality and accuracy of transcripts generated from [a previous] short-read assembly,” the scientists report. The new transcripts “provide a more accurate depiction of gene transcription and will greatly improve C. sinensis genome annotation in the future.”

Subscribe for blog updates:

Archives